Results are preliminary
Low precision for some parameters.
Primary author: Manon Ragonnet and Erik Volz
Report prepared on 2020-04-09 (updated April 20, 2020 )
Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team
This is analysis is based on :
- 152 whole genomes sampled from within Washington
- 68 whole genomes sampled from outside of Washington
- Samples within Washington were collected between 2020-02-26 and 2020-03-15
How many are infected in Washington?
Figure 1: Estimated cumulative infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Washington. The dashed line indicates the date of last sample in Washington in this analysis.
Estimated cumulative infections at last sample (2020-03-15): 12726 [3899-71563] median [95%CI]
Cumulative confirmed infections reported at 2020-03-15: 3745
Figure 2: Estimated daily infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Washington. The dashed line indicates the date of last sample in Washington in this analysis.
Figure 3: Estimated percentage of daily cases reported in Washington. Error bars represent the 95% credible interval.
*Figure 4: Reproduction number through time. The black vertical dashed line indicates the date of last sample in Washington in this analysis. Orange and red dashed lines indicate dates of school closure and general lockdown in Washington, respectively. *
Reproduction number at last sample (2020-03-26): 2.5 [0.94-3.02] median [95% CrI]
How quickly has the epidemic in Washington grown?
|Quantile||Reproduction number||Growth rate (per day)||Doubling time (days)|
Table 1: Reproduction number, growth rate and doubling times
How has SARS-CoV 2 evolved in Washington?
Figure 4: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within Washington, blue tips from outside.
Molecular clock rate of evolution: 0.00167 [0.00119-0.00247] median [95% CrI]
Details on methods and priors can be found here.
Model version: seijr0.0.0
Report version: 20200420-230114-2d0c42b0
Estimates are based on 10 chains with 20 million iterations and 50% burn-in. Effective sample size values
This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.